FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2982582015> ?p ?o ?g. }

• W2982582015 abstract "Abstract Annotating cell types is a critical step in single cell RNA-Seq (scRNA-Seq) data analysis. Some supervised/semi-supervised classification methods have recently emerged to enable automated cell type identification. However, comprehensive evaluations of these methods are lacking to provide practical guidelines. Moreover, it is not clear whether some classification methods originally designed for analyzing other bulk omics data are adaptable to scRNA-Seq analysis. In this study, we evaluated ten cell-type annotation methods publicly available as R packages. Eight of them are popular methods developed specifically for single cell research (Seurat, scmap, SingleR, CHETAH, SingleCellNet, scID, Garnett, SCINA). The other two methods are repurposed from deconvoluting DNA methylation data: Linear Constrained Projection (CP) and Robust Partial Correlations (RPC). We conducted systematic comparisons on a wide variety of public scRNA-seq datasets as well as simulation data. We assessed the accuracy through intra-dataset and inter-dataset predictions, the robustness over practical challenges such as gene filtering, high similarity among cell types, and increased classification labels, as well as the capabilities on rare and unknown cell-type detection. Overall, methods such as Seurat, SingleR, CP, RPC and SingleCellNet performed well, with Seurat being the best at annotating major cell types. Also, Seurat, SingleR, CP and RPC are more robust against down-sampling. However, Seurat does have a major drawback at predicting rare cell populations, and it is suboptimal at differentiating cell types that are highly similar to each other, while SingleR and RPC are much better in these aspects. All the codes and data are available at: https://github.com/qianhuiSenn/scRNA_cell_deconv_benchmark ." @default.
• W2982582015 created "2019-11-08" @default.
• W2982582015 creator A5005523854 @default.
• W2982582015 creator A5018073672 @default.
• W2982582015 creator A5022138363 @default.
• W2982582015 creator A5059709774 @default.
• W2982582015 date "2019-11-01" @default.
• W2982582015 modified "2023-10-05" @default.
• W2982582015 title "Evaluation of Cell Type Annotation R Packages on Single Cell RNA-seq Data" @default.
• W2982582015 cites W1985987855 @default.
• W2982582015 cites W2028426093 @default.
• W2982582015 cites W2137605677 @default.
• W2982582015 cites W2169556367 @default.
• W2982582015 cites W2260409121 @default.
• W2982582015 cites W2297381334 @default.
• W2982582015 cites W2338756998 @default.
• W2982582015 cites W2526262591 @default.
• W2982582015 cites W2551194178 @default.
• W2982582015 cites W2615816755 @default.
• W2982582015 cites W2775981375 @default.
• W2982582015 cites W2794480084 @default.
• W2982582015 cites W2796170779 @default.
• W2982582015 cites W2798368076 @default.
• W2982582015 cites W2801443765 @default.
• W2982582015 cites W2894687190 @default.
• W2982582015 cites W2907514116 @default.
• W2982582015 cites W2916020270 @default.
• W2982582015 cites W2948469692 @default.
• W2982582015 cites W2949067670 @default.
• W2982582015 cites W2949177718 @default.
• W2982582015 cites W2949829455 @default.
• W2982582015 cites W2950086703 @default.
• W2982582015 cites W2951506174 @default.
• W2982582015 cites W2951914955 @default.
• W2982582015 cites W2952148401 @default.
• W2982582015 cites W2959295202 @default.
• W2982582015 cites W2966569571 @default.
• W2982582015 cites W2967290233 @default.
• W2982582015 cites W2971398276 @default.
• W2982582015 cites W2971653850 @default.
• W2982582015 cites W2979142892 @default.
• W2982582015 cites W2979670855 @default.
• W2982582015 cites W2980495984 @default.
• W2982582015 cites W2984472267 @default.
• W2982582015 cites W3006566541 @default.
• W2982582015 cites W3126635526 @default.
• W2982582015 cites W4244030505 @default.
• W2982582015 doi "https://doi.org/10.1101/827139" @default.
• W2982582015 hasPublicationYear "2019" @default.
• W2982582015 type Work @default.
• W2982582015 sameAs 2982582015 @default.
• W2982582015 citedByCount "3" @default.
• W2982582015 countsByYear W29825820152020 @default.
• W2982582015 countsByYear W29825820152021 @default.
• W2982582015 crossrefType "posted-content" @default.
• W2982582015 hasAuthorship W2982582015A5005523854 @default.
• W2982582015 hasAuthorship W2982582015A5018073672 @default.
• W2982582015 hasAuthorship W2982582015A5022138363 @default.
• W2982582015 hasAuthorship W2982582015A5059709774 @default.
• W2982582015 hasBestOaLocation W29825820151 @default.
• W2982582015 hasConcept C104317684 @default.
• W2982582015 hasConcept C116834253 @default.
• W2982582015 hasConcept C124101348 @default.
• W2982582015 hasConcept C138958017 @default.
• W2982582015 hasConcept C1491633281 @default.
• W2982582015 hasConcept C153180895 @default.
• W2982582015 hasConcept C154945302 @default.
• W2982582015 hasConcept C189014844 @default.
• W2982582015 hasConcept C199360897 @default.
• W2982582015 hasConcept C2776321320 @default.
• W2982582015 hasConcept C41008148 @default.
• W2982582015 hasConcept C54355233 @default.
• W2982582015 hasConcept C55493867 @default.
• W2982582015 hasConcept C59822182 @default.
• W2982582015 hasConcept C63479239 @default.
• W2982582015 hasConcept C86803240 @default.
• W2982582015 hasConceptScore W2982582015C104317684 @default.
• W2982582015 hasConceptScore W2982582015C116834253 @default.
• W2982582015 hasConceptScore W2982582015C124101348 @default.
• W2982582015 hasConceptScore W2982582015C138958017 @default.
• W2982582015 hasConceptScore W2982582015C1491633281 @default.
• W2982582015 hasConceptScore W2982582015C153180895 @default.
• W2982582015 hasConceptScore W2982582015C154945302 @default.
• W2982582015 hasConceptScore W2982582015C189014844 @default.
• W2982582015 hasConceptScore W2982582015C199360897 @default.
• W2982582015 hasConceptScore W2982582015C2776321320 @default.
• W2982582015 hasConceptScore W2982582015C41008148 @default.
• W2982582015 hasConceptScore W2982582015C54355233 @default.
• W2982582015 hasConceptScore W2982582015C55493867 @default.
• W2982582015 hasConceptScore W2982582015C59822182 @default.
• W2982582015 hasConceptScore W2982582015C63479239 @default.
• W2982582015 hasConceptScore W2982582015C86803240 @default.
• W2982582015 hasLocation W29825820151 @default.
• W2982582015 hasOpenAccess W2982582015 @default.
• W2982582015 hasPrimaryLocation W29825820151 @default.
• W2982582015 hasRelatedWork W2218034408 @default.
• W2982582015 hasRelatedWork W2263699433 @default.
• W2982582015 hasRelatedWork W2358755282 @default.
• W2982582015 hasRelatedWork W2361861616 @default.
• W2982582015 hasRelatedWork W2377979023 @default.

• next